import dataclasses
import re
import string
from typing import Any, Dict, Iterator, List, Mapping, Optional, Sequence, Tuple

import numpy as np

from . import residue_constants


__a    :	Optional[Any]         =    Mapping[str, np.ndarray]
__a    :	Union[str, Any]         =    Mapping[str, Any]  # Is a nested dict.
__a    :	List[Any]         =    0.01




@dataclasses.dataclass(frozen=_UpperCAmelCase					)
class   _UpperCamelCase :


			"""simple docstring"""






			__a    :					np.ndarray  # [num_res, num_atom_type, 3]

			# Amino-acid type for each residue represented as an integer between 0 and
			# 20, where 20 is 'X'.
			__a    :					np.ndarray  # [num_res]

			# Binary float mask to indicate presence of a particular atom. 1.0 if an atom
			# is present and 0.0 if not. This should be used for loss masking.
			__a    :					np.ndarray  # [num_res, num_atom_type]

			# Residue index as used in PDB. It is not necessarily continuous or 0-indexed.
			__a    :					np.ndarray  # [num_res]

			# B-factors, or temperature factors, of each residue (in sq. angstroms units),
			# representing the displacement of the residue from its ground truth mean
			# value.
			__a    :					np.ndarray  # [num_res, num_atom_type]

			# Chain indices for multi-chain predictions
			__a    :					Optional[np.ndarray]     					=		None

			# Optional remark about the protein. Included as a comment in output PDB
			# files
			__a    :					Optional[str]     					=		None

			# Templates used to generate this protein (prediction-only)
			__a    :					Optional[Sequence[str]]     					=		None

			# Chain corresponding to each parent
			__a    :					Optional[Sequence[int]]     					=		None





def 							UpperCAmelCase		(       lowercase				):







				"""simple docstring"""



				__lowercase					     =				r'''(\[[A-Z]+\]\n)'''
				__lowercase					     =				[tag.strip() for tag in re.split(lowercase				,     lowercase				) if len(lowercase				) > 0]
				__lowercase					     =				zip(tags[0::2]				,     [l.split('''\n'''				) for l in tags[1::2]]				)

				__lowercase					     =				["N", "CA", "C"]
				__lowercase					     =				None
				__lowercase					     =				None
				__lowercase					     =				None
				for g in groups:
								if "[PRIMARY]" == g[0]:
												__lowercase					     =				g[1][0].strip()
												for i in range(len(lowercase				)				):
																if seq[i] not in residue_constants.restypes:
																				__lowercase					     =				'''X'''  # FIXME: strings are immutable
												__lowercase					     =				np.array(
												    [residue_constants.restype_order.get(lowercase				,     residue_constants.restype_num				) for res_symbol in seq]				)
								elif "[TERTIARY]" == g[0]:
												__lowercase					     =				[]
												for axis in range(3				):
																tertiary.append(list(map(lowercase				,     g[1][axis].split()				)				)				)
												__lowercase					     =				np.array(lowercase				)
												__lowercase					     =				np.zeros((len(tertiary[0]				) // 3, residue_constants.atom_type_num, 3)				).astype(np.floataa				)
												for i, atom in enumerate(lowercase				):
																__lowercase					     =				np.transpose(tertiary_np[:, i::3]				)
												atom_positions *= PICO_TO_ANGSTROM
								elif "[MASK]" == g[0]:
												__lowercase					     =				np.array(list(map({'''-''': 0, '''+''': 1}.get				,     g[1][0].strip()				)				)				)
												__lowercase					     =				np.zeros(
												    (
												        len(lowercase				),
												        residue_constants.atom_type_num,
												    )				).astype(np.floataa				)
												for i, atom in enumerate(lowercase				):
																__lowercase					     =				1
												atom_mask *= mask[..., None]

				assert aatype is not None

				return Protein(
				    atom_positions=lowercase				,     atom_mask=lowercase				,     aatype=lowercase				,     residue_index=np.arange(len(lowercase				)				)				,     b_factors=lowercase				,     )





def 							UpperCAmelCase		(       lowercase				,     lowercase = 0				):







				"""simple docstring"""



				__lowercase					     =				[]

				__lowercase					     =				prot.remark
				if remark is not None:
								pdb_headers.append(F"REMARK {remark}"				)

				__lowercase					     =				prot.parents
				__lowercase					     =				prot.parents_chain_index
				if parents is not None and parents_chain_index is not None:
								__lowercase					     =				[p for i, p in zip(lowercase				,     lowercase				) if i == chain_id]

				if parents is None or len(lowercase				) == 0:
								__lowercase					     =				['''N/A''']

				pdb_headers.append(F"PARENT {' '.join(lowercase				)}"				)

				return pdb_headers





def 							UpperCAmelCase		(       lowercase				,     lowercase				):







				"""simple docstring"""



				__lowercase					     =				[]
				__lowercase					     =				pdb_str.split('''\n'''				)

				__lowercase					     =				prot.remark
				if remark is not None:
								out_pdb_lines.append(F"REMARK {remark}"				)

				__lowercase					     =				42
				if prot.parents is not None and len(prot.parents				) > 0:
								__lowercase					     =				[]
								if prot.parents_chain_index is not None:
												__lowercase					     =				{}
												for p, i in zip(prot.parents				,     prot.parents_chain_index				):
																parent_dict.setdefault(str(lowercase				)				,     []				)
																parent_dict[str(lowercase				)].append(lowercase				)

												__lowercase					     =				max([int(lowercase				) for chain_idx in parent_dict]				)
												for i in range(max_idx + 1				):
																__lowercase					     =				parent_dict.get(str(lowercase				)				,     ['''N/A''']				)
																parents_per_chain.append(lowercase				)
								else:
												parents_per_chain.append(list(prot.parents				)				)
				else:
								__lowercase					     =				[['''N/A''']]

				def make_parent_line(lowercase				) -> str:
								return F"PARENT {' '.join(lowercase				)}"

				out_pdb_lines.append(make_parent_line(parents_per_chain[0]				)				)

				__lowercase					     =				0
				for i, l in enumerate(lowercase				):
								if "PARENT" not in l and "REMARK" not in l:
												out_pdb_lines.append(lowercase				)
								if "TER" in l and "END" not in lines[i + 1]:
												chain_counter += 1
												if not chain_counter >= len(lowercase				):
																__lowercase					     =				parents_per_chain[chain_counter]
												else:
																__lowercase					     =				['''N/A''']

												out_pdb_lines.append(make_parent_line(lowercase				)				)

				return "\n".join(lowercase				)





def 							UpperCAmelCase		(       lowercase				):







				"""simple docstring"""



				__lowercase					     =				residue_constants.restypes + ['''X''']

				def res_atoa(lowercase				) -> str:
								return residue_constants.restype_atoa.get(restypes[r]				,     '''UNK'''				)

				__lowercase					     =				residue_constants.atom_types

				__lowercase					     =				[]

				__lowercase					     =				prot.atom_mask
				__lowercase					     =				prot.aatype
				__lowercase					     =				prot.atom_positions
				__lowercase					     =				prot.residue_index.astype(np.intaa				)
				__lowercase					     =				prot.b_factors
				__lowercase					     =				prot.chain_index

				if np.any(aatype > residue_constants.restype_num				):
								raise ValueError('''Invalid aatypes.'''				)

				__lowercase					     =				get_pdb_headers(lowercase				)
				if len(lowercase				) > 0:
								pdb_lines.extend(lowercase				)

				__lowercase					     =				aatype.shape[0]
				__lowercase					     =				1
				__lowercase					     =				0
				__lowercase					     =				string.ascii_uppercase
				__lowercase					     =				None
				# Add all atom sites.
				for i in range(lowercase				):
								__lowercase					     =				res_atoa(aatype[i]				)
								for atom_name, pos, mask, b_factor in zip(lowercase				,     atom_positions[i]				,     atom_mask[i]				,     b_factors[i]				):
												if mask < 0.5:
																continue

												__lowercase					     =				'''ATOM'''
												__lowercase					     =				atom_name if len(lowercase				) == 4 else F" {atom_name}"
												__lowercase					     =				''''''
												__lowercase					     =				''''''
												__lowercase					     =				1.00
												__lowercase					     =				atom_name[0]  # Protein supports only C, N, O, S, this works.
												__lowercase					     =				''''''

												__lowercase					     =				'''A'''
												if chain_index is not None:
																__lowercase					     =				chain_tags[chain_index[i]]

												# PDB is a columnar format, every space matters here!
												__lowercase					     =				(
												    F"{record_type:<6}{atom_index:>5} {name:<4}{alt_loc:>1}"
												    F"{res_name_a:>3} {chain_tag:>1}"
												    F"{residue_index[i]:>4}{insertion_code:>1}   "
												    F"{pos[0]:>8.3f}{pos[1]:>8.3f}{pos[2]:>8.3f}"
												    F"{occupancy:>6.2f}{b_factor:>6.2f}          "
												    F"{element:>2}{charge:>2}"
												)
												pdb_lines.append(lowercase				)
												atom_index += 1

								__lowercase					     =				i == n - 1
								if chain_index is not None:
												if i != n - 1 and chain_index[i + 1] != prev_chain_index:
																__lowercase					     =				True
																__lowercase					     =				chain_index[i + 1]

								if should_terminate:
												# Close the chain.
												__lowercase					     =				'''TER'''
												__lowercase					     =				(
												    F"{chain_end:<6}{atom_index:>5}      {res_atoa(aatype[i]				):>3} {chain_tag:>1}{residue_index[i]:>4}"
												)
												pdb_lines.append(lowercase				)
												atom_index += 1

												if i != n - 1:
																# "prev" is a misnomer here. This happens at the beginning of
																# each new chain.
																pdb_lines.extend(get_pdb_headers(lowercase				,     lowercase				)				)

				pdb_lines.append('''END'''				)
				pdb_lines.append(''''''				)
				return "\n".join(lowercase				)





def 							UpperCAmelCase		(       lowercase				):







				"""simple docstring"""



				return residue_constants.STANDARD_ATOM_MASK[prot.aatype]





def 							UpperCAmelCase		(       lowercase				,     lowercase				,     lowercase = None				,     lowercase = None				,     lowercase = None				,     lowercase = None				,     lowercase = None				,     ):







				"""simple docstring"""



				return Protein(
				    aatype=features['''aatype''']				,     atom_positions=result['''final_atom_positions''']				,     atom_mask=result['''final_atom_mask''']				,     residue_index=features['''residue_index'''] + 1				,     b_factors=b_factors if b_factors is not None else np.zeros_like(result['''final_atom_mask''']				)				,     chain_index=lowercase				,     remark=lowercase				,     parents=lowercase				,     parents_chain_index=lowercase				,     )
def 							UpperCAmelCase		(       lowercase				,     lowercase				):







				"""simple docstring"""



				__lowercase					     =				word.split()

				def justify(lowercase				,     lowercase				,     lowercase				) -> str:
								__lowercase					     =				max_width - width
								__lowercase					     =				len(lowercase				)
								if len(lowercase				) == 1:
												# if there is only word in line
												# just insert overall_spaces_count for the remainder of line
												return line[0] + " " * overall_spaces_count
								else:
												__lowercase					     =				words_count - 1
												# num_spaces_between_words_list[i] : tells you to insert
												# num_spaces_between_words_list[i] spaces
												# after word on line[i]
												__lowercase					     =				spaces_to_insert_between_words * [
												    overall_spaces_count // spaces_to_insert_between_words
												]
												__lowercase					     =				(
												    overall_spaces_count % spaces_to_insert_between_words
												)
												# distribute spaces via round robin to the left words
												for i in range(lowercase				):
																num_spaces_between_words_list[i] += 1
												__lowercase					     =				[]
												for i in range(lowercase				):
																# add the word
																aligned_words_list.append(line[i]				)
																# add the spaces to insert
																aligned_words_list.append(num_spaces_between_words_list[i] * ''' '''				)
												# just add the last word to the sentence
												aligned_words_list.append(line[-1]				)
												# join the aligned words list to form a justified line
												return "".join(lowercase				)

				__lowercase					     =				[]
				__lowercase					     =				[]
				__lowercase					     =				0
				for word in words:
								if width + len(lowercase				) + len(lowercase				) <= max_width:
												# keep adding words until we can fill out max_width
												# width = sum of length of all words (without overall_spaces_count)
												# len(word) = length of current word
												# len(line) = number of overall_spaces_count to insert between words
												line.append(lowercase				)
												width += len(lowercase				)
								else:
												# justify the line and add it to result
												answer.append(justify(lowercase				,     lowercase				,     lowercase				)				)
												# reset new line and new width
												__lowercase     ,	__lowercase					     =				[word], len(lowercase				)
				__lowercase					     =				max_width - width - len(lowercase				)
				answer.append(''' '''.join(lowercase				) + (remaining_spaces + 1) * ''' '''				)
				return answer


if __name__ == "__main__":
		from doctest import testmod

		testmod()